Simultaneous determination of tin, germanium and molybdenum in food samples has been established by flow injection-charge coupled detector (CCD) diode array detection spectrophotometry with partial least squares (PLS) algorithm. The methodwas based on the chromogenic reaction of metal ions and salicylflurone in the presence of cetyltrimethyl ammonium bromide. The overlapping spectra of these complexes are collected by CCD diode array detector and the multi-wavelength absorbance data are processed using partial least squares algorithm. The reaction conditions and analytical parameters of flow injection analysis have been investigated. The method was applied to directly determine Ge, Mo and Sn in several food samples after digestion with satisfactory results. The recoveries of spiked samples were 80.0-102.0% for tin, 86.3-92.0% for germanium and 83.2-95.2% for molybdenum, and the relative standard deviations for samples were 4.4-7.8%. Molybdenum in certified reference material of cattle liver was determined by the proposed method (n=8). The differential values between determined and guarantee values were within the given uncertain value ranges (t=1.687,P>0.05 for t-test). The samples of mung bean, kelp and pork liver were analyzed by the proposed method and inductively couple plasma-atomic emission spectroscopy (ICP-AES) method. The determination results of the two methods are in good agreement. The sampling rate is 30 samples h−1.